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From 02/27/2019 to 03/28/2019

03/28/2019

07:55 PM feature request #7860: [Master] Remaining E+M editor issues
Urgent for E+M and therefore should be handled latest in 5.7. But especially important is the task covered by #7920 Andreas Müller
07:52 PM feature request #7920: Possibility to define area specific status selection
This is urgent for E+M and should be handled very soon. Latest in 5.7 but if possible in 5.6 Andreas Müller
07:34 PM task #7455 (Resolved): [Check] Check all markers for correctnes
After import we should still check if need those markers with small count. Therefore do not close completely. Andreas Müller
02:09 PM feature request #7865 (Resolved): Remaining factual data view label issues
this should be fixed by fixing #8200 Patrick Plitzner
02:08 PM bug #8200 (Resolved): Changing title(cache) for factual data set not possible
I replaced the label with a toggleable cache field.
How it works now: When setting the cache to unprotected (closi...
Patrick Plitzner
10:59 AM bug #8211 (Closed): Trigger new search when clicking on identifier search
in reference search dialog a new search should be triggered if identifier search is clicked Katja Luther
10:09 AM bug #8210 (New): During search in bulk editor it is not possible to select items
As running a search is done in another thread and the list is updated asynchronously it is not possible to select an ... Patrick Plitzner
08:47 AM task #8209 (Resolved): use ellypsed references for all reference comboboxes
use the `ReferenceEllypsisFormatter` which has been implemented for #7951 in all reference comboboxes Andreas Kohlbecker
08:40 AM bug #8050: Create blocking registrations for un-registered names which are to be used in nomencla...
Wolf-Henning Kusber wrote:
> Solution 1 should also preclude name duplicates.
this should be handled in a separat...
Andreas Kohlbecker
08:39 AM feature request #8121 (Resolved): Allow selecting structural/property modifiers when creating a c...
Patrick Plitzner
08:39 AM feature request #8208 (New): Allow selecting property modifiers when creating a character
copied from #8121 Patrick Plitzner
08:38 AM feature request #8207 (New): RegistrationUI: helps avoid name duplicates
When ever a user is about to create a new name, the system should check for potential duplicates of the name to be cr... Andreas Kohlbecker
08:34 AM feature request #7923 (Resolved): Add context menu and drag'n'drop to CharacterEditor
Patrick Plitzner
08:33 AM feature request #8146 (Resolved): Adapt taxeditor UI to structure and property term type
Patrick Plitzner
08:27 AM feature request #8011 (Resolved): Implement term search view
Patrick Plitzner

03/27/2019

05:59 PM task #7798: [AM, ERS]: Import (freetext) nameInSource correctly
Eckhard noch fragen, was mit den Namen geschehen soll, bei denen LinkedName und FreeTextName nicht übereinstimmen.
D...
Andreas Müller
05:58 PM task #7798: [AM, ERS]: Import (freetext) nameInSource correctly
ERS decided to use synonymie names whereever possible. Equalness of existence of authors is not so important.
With t...
Andreas Müller
05:57 PM bug #8050: Create blocking registrations for un-registered names which are to be used in nomencla...
Solution 1 should also preclude name duplicates. Wolf-Henning Kusber
05:36 PM bug #8050 (In Progress): Create blocking registrations for un-registered names which are to be us...
We agreed on solution 1. from above: "*Require the user to add a reference to the name before the popup editor in whi... Andreas Kohlbecker
01:12 PM bug #8050 (Feedback): Create blocking registrations for un-registered names which are to be used ...
There will be situations in which the existing name will not yet have a nomenclatural reference. Creating a Registrat... Andreas Kohlbecker
05:36 PM feature request #7894 (Resolved): [CHECK] Import sourceNumber as Identifier for references
Andreas Müller
04:32 PM bug #7963: TaxonNamePopEditor: name part field visibility not correct for all ranks
done!
For the rank "unknown rank" only the uninomial field is shown
For the remaining tasks formulated in the d...
Andreas Kohlbecker
04:16 PM bug #7963 (Resolved): TaxonNamePopEditor: name part field visibility not correct for all ranks
Applied in changeset commit:cdm-vaadin|a0643e2c0aa12a7c83f208bf2709dc06a163befb. Andreas Kohlbecker
03:54 PM bug #8197 (Closed): Deleting Media from Image Gallery View does not make view dirty
works fine Patrick Plitzner
02:45 PM bug #8197 (Resolved): Deleting Media from Image Gallery View does not make view dirty
this should be fixed now. The operation is executed while saving now. Katja Luther
03:47 PM task #7935 (Feedback): Discuss new solution to establish the communication between submitter and ...
Hi Henning,
is there anything left to discuss regarding this issue?
Andreas
Andreas Kohlbecker
03:44 PM feature request #7968 (Closed): ReferenceEditor: optional validation for completenes of Partial v...
fully implemented but untestable since the system apparently does not allow to use incomplete Partials in the vaadin UI. Andreas Kohlbecker
03:42 PM feature request #7968 (Resolved): ReferenceEditor: optional validation for completenes of Partial...
Applied in changeset commit:cdm-vaadin|f8fda7a9f00c1e87430c03d06bbcfcff44aa7ff4. Andreas Kohlbecker
02:56 PM feature request #7968 (In Progress): ReferenceEditor: optional validation for completenes of Part...
Andreas Kohlbecker
03:00 PM bug #7833 (Rejected): submitters can access see any registration in any RegistrationWorkingSet
Andreas Kohlbecker
02:27 PM bug #8206 (New): Editing references with missing update rights should not be possible
Actually it is possible to edit references without the UPDATE right for references. While saving the user gets an exc... Katja Luther

03/26/2019

05:14 PM bug #8050: Create blocking registrations for un-registered names which are to be used in nomencla...
Wenn man versehentlich einen falschen namen z.B. als Basionym auswählt, würde dann für diesen Namen eine Blocking-Reg... Andreas Kohlbecker
03:57 PM bug #8149 (Closed): ReferenceEditor: filter inReferences ONLY by applicable reference type suppes...
Henning, says this is tested and works as expected. Andreas Kohlbecker
03:55 PM bug #8194 (Closed): LazyInitializationException (LIE) on deleting the nomenclatural referenz (Se...
Andreas Kohlbecker
03:54 PM bug #8194: LazyInitializationException (LIE) on deleting the nomenclatural referenz (Section) of...
We agreed on :
> 1. hide the delete button in this situation and implement #8204
Warning is sufficient, we don'...
Andreas Kohlbecker
03:53 PM feature request #8204: RegistrationWorkingsetEditor shows list of unused sections and allows for ...
nice to have Andreas Kohlbecker
03:48 PM bug #4545 (Closed): Implement TeamOrPersonBaseSelectionDialog
The selection dialog works like the other selection dialogs. Institution, as the only sub class of AgentBase that sho... Patrick Plitzner
03:44 PM bug #8191 (Closed): ReferencePopupEditor: When coming from NameEdior editing of the inreference s...
Andreas Kohlbecker
03:38 PM bug #8197 (Feedback): Deleting Media from Image Gallery View does not make view dirty
Now the name editor is set to dirty but if it is closed without saving the media is removed anyways. So either the me... Patrick Plitzner
08:47 AM bug #8197: Deleting Media from Image Gallery View does not make view dirty
this should be fixed, please review. Katja Luther
03:30 PM bug #8192 (Closed): The curator must be able to unlock a published registration for edition
Andreas Kohlbecker
09:19 AM bug #8115: NPE when moving factual data
this is because the description only contains a not persisted description element and this is not available when the ... Katja Luther

03/25/2019

06:58 PM bug #8192: The curator must be able to unlock a published registration for edition
Checked in Test-System with two names of Nupela, registered 2018-11-02.
TypeSpecimen: unlock and add a type: works...
Wolf-Henning Kusber
02:50 PM bug #8192 (Resolved): The curator must be able to unlock a published registration for edition
done, please review Andreas Kohlbecker
05:46 PM bug #8191: ReferencePopupEditor: When coming from NameEdior editing of the inreference should not...
I was able to include new journal names in Basionym references. I included sections in the name editor and was able t... Wolf-Henning Kusber
02:51 PM bug #8191 (Resolved): ReferencePopupEditor: When coming from NameEdior editing of the inreference...
please review Andreas Kohlbecker
05:28 PM bug #8050 (In Progress): Create blocking registrations for un-registered names which are to be us...
Andreas Kohlbecker
04:45 PM bug #7962: PopupEditors: *DTO in context 'breadcrumbs' to be transformed into more humane labels
Please review Andreas Kohlbecker
04:42 PM bug #7962 (Resolved): PopupEditors: *DTO in context 'breadcrumbs' to be transformed into more hu...
Applied in changeset commit:cdm-vaadin|8745f04714df865f1780025b43b24b9eaa5a198a. Andreas Kohlbecker
02:17 PM feature request #8033 (Duplicate): Add/Enable absent/present state for every character
duplicates #8178 Patrick Plitzner
10:12 AM feature request #8153: Adapt cdmlib to FeatureNode/FeatureTree model changes
By introducing the generics this is probably done. There is still some code which does not use/specify generics but t... Patrick Plitzner

03/22/2019

07:58 PM bug #8075 (Resolved): multiple cascade all-delete-orphan exceptions related to DefinedTermBase.re...
Andreas Kohlbecker
07:49 PM bug #8075: multiple cascade all-delete-orphan exceptions related to DefinedTermBase.representations
potentially fixed through the changes made for #8160, #7106 Andreas Kohlbecker
07:57 PM bug #8158 (Resolved): cascade="all-delete-orphan" problem when ....
potentially fixed through the changes made for #8160, #7106 Andreas Kohlbecker
07:56 PM bug #7881 (Resolved): reference selection combobox broken after error in ...
potentially fixed through the changes made for #8160, #7106 Andreas Kohlbecker
07:51 PM bug #8065 (Feedback): HibernateException: corrupt session problem breaks SpecimenTypeDesignationw...
potentially fixed through the changes made for #8160, #7106 Andreas Kohlbecker
07:20 PM bug #8149: ReferenceEditor: filter inReferences ONLY by applicable reference type suppess Generic...
please review Andreas Kohlbecker
07:18 PM bug #8149 (Resolved): ReferenceEditor: filter inReferences ONLY by applicable reference type supp...
Applied in changeset commit:cdm-vaadin|27820075a6585b46648a6f1dcd4241a6b45596d8. Andreas Kohlbecker
07:19 PM bug #8184: SpecimenTypedesignationEditor: add new specimen broken Chrome browser
please review with Heba if this still occurs Andreas Kohlbecker
07:18 PM bug #8184 (Resolved): SpecimenTypedesignationEditor: add new specimen broken Chrome browser
Applied in changeset commit:cdm-vaadin|86f09e7b2e34f272b2f4769f5f7fb3729fea7ef7. Andreas Kohlbecker
07:18 PM bug #8184: SpecimenTypedesignationEditor: add new specimen broken Chrome browser
this seems to be a bug in the ListSelect which affects the Chrome browser Andreas Kohlbecker
06:28 PM feature request #8180 (In Progress): Add property term "Presence/Absence" to CDM default terms
Andreas Müller
06:28 PM feature request #8153 (Feedback): Adapt cdmlib to FeatureNode/FeatureTree model changes
is this still an open issue? If yes, can you give more inside? Andreas Müller
06:13 PM bug #8183 (In Progress): Make Feature IndividualAssociation a generalization of Specimen and Obse...
Andreas Müller
04:35 PM bug #8205 (New): SpecimenTypeDesignationsEditor: Fist selection of mediaReference gets lost
Permanent bug:
Image Reference is selected for the first time -> selected but not gets lost when clicking in another...
Wolf-Henning Kusber
03:51 PM bug #8194 (Feedback): LazyInitializationException (LIE) on deleting the nomenclatural referenz (...
Even if the LazyInitializationException is avoided deletion of the section is impossible since it is still in use as ... Andreas Kohlbecker
03:32 PM bug #8115: NPE when moving factual data
I just tested it with cdmlib and taxeditor completely up-to-date. I tested on a copy of flora of greece this time to ... Patrick Plitzner
02:06 PM bug #8115: NPE when moving factual data
Did you test with the actual cdmlib version?
cdmlib was not build until this morning.
Katja Luther
01:46 PM bug #8115 (Feedback): NPE when moving factual data
Now saving in step 4 works but the description with the description from which the element was moved away from disapp... Patrick Plitzner
03:31 PM feature request #8204 (New): RegistrationWorkingsetEditor shows list of unused sections and allow...
the RegistrationUI does not allow deleting unused sections. The RegistrationWorkingsetEditor could show the list of u... Andreas Kohlbecker
03:24 PM bug #8203 (New): Adapt specimen page title to record basis
The current specimen page hast "Specimen" written in the title despite the actual record basis
Example: http://por...
Patrick Plitzner
02:50 PM bug #8202 (New): Multiple representations exception when reusing image in image gallery
In Flora of Greece I tried to move an image from taxon Anchusa aegyptiaca to Anchusella variegata.
I did this by fir...
Andreas Müller
02:39 PM task #8201 (New): test all delete functionality in the RegistrationUI
Andreas Kohlbecker
02:35 PM bug #8200 (Closed): Changing title(cache) for factual data set not possible
When trying to change the title of a factual data set in details view the old title is recreated during save.
Corr...
Andreas Müller
02:32 PM bug #8197 (Resolved): Deleting Media from Image Gallery View does not make view dirty
Applied in changeset commit:taxeditor|02bb31eada6b7edfb3c3d155bb13ad967428aa56. Katja Luther
02:22 PM bug #8197 (Closed): Deleting Media from Image Gallery View does not make view dirty
... therefore one may think that the media is deleted but it is not after reload. This is dangerous therefore high pr... Andreas Müller
02:26 PM feature request #8199 (New): ReferencePage: show the relation of orthographic corrections to the ...
in case of an orthographic correction both names which are related this way belong to the same publication.
In the...
Andreas Kohlbecker
02:24 PM bug #8198 (New): Deleting an image gallery from image gallery view shows wrong configuration dialog
It shows the same dialog like when deleting media, but the image gallery is something else. Image galleries should no... Andreas Müller
02:16 PM feature request #8196 (In Progress): display ortographic corrections in name relations as 'correc...
ortographic corrections are to be displayed as last entries in the name relations:
* corrected name: <nameCache> [...
Andreas Kohlbecker
01:33 PM feature request #8195 (New): TaxonNamePopupEditor: offer Reference and RuleConsidered fields for ...
in contrast to earlier considerations for *Replaced Synonyms* it is also important to enter data into the Reference a... Andreas Kohlbecker
09:08 AM bug #8190 (Resolved): Default FeatureTree throws exception
I extended the type check to also allow subtypes in the term tree Patrick Plitzner

03/21/2019

07:03 PM bug #8192: The curator must be able to unlock a published registration for edition
use the lock and unlock icons from fontawesome:
https://fontawesome.com/icons/lock-open?style=solid
https://fon...
Andreas Kohlbecker
06:32 PM bug #8192 (Closed): The curator must be able to unlock a published registration for edition
The curator sometimes needs to modify the data for a registration after it has been published.
Currently it is req...
Andreas Kohlbecker
07:01 PM bug #8194: LazyInitializationException (LIE) on deleting the nomenclatural referenz (Section) of...
Initializing the authorteam of the inReferences of the references loaded by the combobox should solve the problem. Andreas Kohlbecker
06:59 PM bug #8194 (Closed): LazyInitializationException (LIE) on deleting the nomenclatural referenz (Se...

Habe die Section des eines Namens die als nomenklatorische Referenz gesetzt war löschen wollen:
http://phycoba...
Andreas Kohlbecker
06:46 PM feature request #8193 (Closed): TaxonNamePopupEditor: add select form element for Nomenclatural s...
Enable to add a nomenclatural status from a subset of status (see TaxEditor).
Exception invalid name in valitation =...
Wolf-Henning Kusber
06:26 PM bug #8191 (Closed): ReferencePopupEditor: When coming from NameEdior editing of the inreference s...
By now when opening the ReferenceEditor for inReference of a TaxonName the user can not modify or set a new inreferen... Andreas Kohlbecker
04:25 PM bug #8189 (Resolved): Allow configuration of 'user.home' via the spring environment
close issue if the changes are not causing any problems. Andreas Kohlbecker
12:15 PM bug #8189 (Closed): Allow configuration of 'user.home' via the spring environment
By now it is only possible to configure the `${user.home}` via the system properties. That means the only option to s... Andreas Kohlbecker
03:03 PM bug #8190 (In Progress): Default FeatureTree throws exception
Patrick Plitzner
01:30 PM bug #8190 (Closed): Default FeatureTree throws exception
When there are Characters and Features in the data base and the default feature tree is created it will fetch all of ... Patrick Plitzner
02:56 PM feature request #8058: Further issues for (local) preferences
the common name language preference is added. Katja Luther
11:43 AM bug #8184: SpecimenTypedesignationEditor: add new specimen broken Chrome browser
Specimen Editor: auch der erste Typus lässt sich nicht speichern (kritisch)
Andreas Kohlbecker

03/20/2019

04:41 PM feature request #7975: Implement a block to display name relations
Validation:
![](picture156-1.png)
Replacement name:
Wie Validation behandeln,
Zudem wird
1. beim Widg...
Andreas Kohlbecker
02:54 PM bug #8188 (In Progress): Allow configuring hibernate properties via properties file
Andreas Kohlbecker
02:54 PM bug #8188 (Closed): Allow configuring hibernate properties via properties file
To allow for more flexible configuration of test environments it would be great if the hibernate properties which are... Andreas Kohlbecker
11:10 AM feature request #8187 (New): Use Spring Environment instead of custom code in AbstractWebApplicat...
the method `AbstractWebApplicationConfigurer.findProperty(String property, boolean required)` implements a similar st... Andreas Kohlbecker

03/19/2019

07:31 PM feature request #7975: Implement a block to display name relations
Examples correctly in PhycoBank as use case for output improvement:
Example Validation
https://www.phycobank.org...
Wolf-Henning Kusber
02:30 PM feature request #7428: Open issues for updating open data while subtree is updated
please review.
Bulkeditor and nameeditor are updated.
Katja Luther
01:36 PM bug #8115 (Resolved): NPE when moving factual data
this problem is fixed. Katja Luther
01:29 PM bug #4545 (Resolved): Implement TeamOrPersonBaseSelectionDialog
please review.
TeamOrPerson is used for example for TaxonNodeAgentRelations or for authors in references
Katja Luther
12:49 PM feature request #8185 (Feedback): Type layout
Hi Andreas, the same kind of formatting has formerly also been requested by Walter.
I consider this a very good so...
Andreas Kohlbecker
09:52 AM feature request #8186 (Duplicate): List view order
ordering by registration numbers is hardly possible, see #7978.
Furthermore is this ticket a duplicate of #8157
Andreas Kohlbecker

03/18/2019

06:02 PM feature request #8186 (Duplicate): List view order
List view in Vaadin should be arranged from new (high registration numbers) to old.
Wolf-Henning Kusber
05:51 PM feature request #8185 (Feedback): Type layout
Type (as is):
Holotype: (BM BM123)
should be:
Holotype: BM (BM123)
see for example: https://www.phycobank...
Wolf-Henning Kusber
05:45 PM bug #8184 (Closed): SpecimenTypedesignationEditor: add new specimen broken Chrome browser
In Vaadin, type specimen editor a new line is created when a typ is selected.
This functions in FireFox. This does n...
Wolf-Henning Kusber
05:16 PM bug #8183 (In Progress): Make Feature IndividualAssociation a generalization of Specimen and Obse...
until now this has been handled in the static method Feature.INDIVIDUALS_ASSOCIATION() which is not the correct place... Andreas Müller
03:55 PM bug #8115 (Feedback): NPE when moving factual data
This setup now works because we have to save before dragging the abstract to the other description
There is howeve...
Patrick Plitzner
02:07 PM task #7515: TypeDesignationStatusComparator to sort by vocabulary first and then by term order
Andreas Kohlbecker wrote:
> The Taxeditor should be more resilient against unusual data.
>
> 1. Suggestion as d...
Katja Luther
01:33 PM feature request #7433: new service method to get specimen by genetic AccessionNumber
this service method is implemented, but controller method is still missing Katja Luther
01:30 PM feature request #8182 (In Progress): show blast search result
the json result of the blast search should be displayed and the accession number needs to be a link to the correspond... Katja Luther
01:20 PM bug #8148 (Resolved): Login Dialog cuts off information
I put it to resolved to remind me reviewing.
Or are there still open issues?
Andreas Müller
01:04 PM bug #8148: Login Dialog cuts off information
I adapted the exception section and I could not reproduce the cutted advanced section (with the actual nightly). Coul... Katja Luther
11:55 AM feature request #5890 (New): Implement auto-suggest for data portal
Patrick Plitzner

03/15/2019

03:29 PM bug #8169: avoid factory.openSession() in DaoBase
VersionableServiceBase.isDeletable misses the @Transactional(readOnly = true) annotation! Andreas Kohlbecker
03:25 PM bug #8169: avoid factory.openSession() in DaoBase
Here is a case found in the server log (occurred 6x in a couple of hours):
~~~
[phycobank] 2019-03-15 10:27:44,...
Andreas Kohlbecker
11:44 AM feature request #8181 (New): Further features for bulk editors
this is a ticket to collect all wanted features for bulkeditors:
Henning:
* further filter options (ref type)
Katja Luther
10:44 AM feature request #7755: Implement advanced detail page for occurrences
mail from AM:
Hallo Katja,
ich bin im Zuge von FoG über die Specimenseite gestolpert. Sehr schön, dass da jetzt...
Katja Luther
09:21 AM feature request #8180 (Closed): Add property term "Presence/Absence" to CDM default terms
When describing a specimen via Characters (almost) all structures may or may not exist. To be able to describe if a s... Patrick Plitzner

03/14/2019

06:26 PM bug #8179 (New): PopupEditorException
Type name editor, PopupEditorException
when saving a name type of a genus
in Workingset
http://api.phycobank.org...
Wolf-Henning Kusber
02:12 PM feature request #8178 (Rejected): Auto-create absence/presence character for every structure
Presence/Absence Property (PA)
* Jede Strukture muss in Kombination mit PA-Property einen Character bilden.
* Bei...
Patrick Plitzner
02:04 PM feature request #8121 (In Progress): Allow selecting structural/property modifiers when creating ...
Patrick Plitzner
01:56 PM feature request #6849 (In Progress): [DISCUSS] How to handle "kind of" term creation in TermEditor
Patrick Plitzner
12:11 PM feature request #6413 (Resolved): [DISCUSS] How to create type duplicates (e.g. isotypes) for a t...
The first implementation allows selection one of the already existing specimen type designation for creating the dupl... Patrick Plitzner

03/13/2019

12:52 PM feature request #8175: add name facts to cdm light export
the name facts are moved to their own table. Katja Luther
09:57 AM feature request #7428 (Resolved): Open issues for updating open data while subtree is updated
Applied in changeset commit:taxeditor|4fff2d21dfed4ae1ba6c5106e7d59cdf2e82548c. Katja Luther
09:36 AM bug #8176 (Resolved): WeaklyRelatedEntityCombobox is slow
test TaxonNamePopupEditor Genus field, replaced Synonym and Basionym also some ToManyRelatedEntitiesComboboxes and T... Andreas Kohlbecker

03/12/2019

05:57 PM bug #8176 (In Progress): WeaklyRelatedEntityCombobox is slow
Andreas Kohlbecker
02:15 PM bug #8176 (Closed): WeaklyRelatedEntityCombobox is slow
## on setting values
The WeaklyRelatedEntityCombobox needs to check if the value to set is at all contained in the...
Andreas Kohlbecker
02:22 PM feature request #8177 (New): Discuss: Mother of a type specimen
How to store? Wolf-Henning Kusber
01:07 PM bug #6627: Remaining cdm light issues
the name facts are implemented now, see #8175 Katja Luther
01:06 PM feature request #8175: add name facts to cdm light export
please review Katja Luther
01:06 PM feature request #8175 (Resolved): add name facts to cdm light export
Applied in changeset commit:cdmlib|852a1a9e5171370a8e3e6962b21837e38115cf9a. Katja Luther
01:04 PM feature request #8175 (Closed): add name facts to cdm light export
We decided to keep the name facts in cdm, so the name facts should be exported as well Katja Luther
12:53 PM bug #8099: Error saving name type designation editor due to problem in poupeditor context
can not reproduce Andreas Kohlbecker
12:03 PM bug #8111: User selection dialog for groups does not filter out existing users
please review Katja Luther
12:02 PM bug #8111 (Resolved): User selection dialog for groups does not filter out existing users
Applied in changeset commit:taxeditor|cbc83794de4303c54b45309ff151c70627e82e1a. Katja Luther
11:34 AM bug #8115: NPE when moving factual data
please review Katja Luther
11:33 AM bug #8115: NPE when moving factual data
the problem was the not persisted description, therefore the description needs to be passed to the service method. To... Katja Luther
11:26 AM bug #8115 (Resolved): NPE when moving factual data
Applied in changeset commit:taxeditor|803af83ee2911d193d6a95a3f73dee727ae77d45. Katja Luther
09:31 AM feature request #8136: Implement sources for type designations in TaxEditor
please review Katja Luther
09:30 AM feature request #8136 (Resolved): Implement sources for type designations in TaxEditor
Applied in changeset commit:taxeditor|9f40979f5e0d2fc55100acc5a7fabac00d48ce12. Katja Luther
08:36 AM bug #8105: better hotfix branch strategy in git flow to avoid commits in master which are missing...
I did a brief research on the topic of hotfix branches:
1. git flow has the concept of *support branches* by which...
Andreas Kohlbecker
08:11 AM task #8130: Check if related feature data is cleared when supported facts type is changed
For nomenclatural code there is a method checkForDeletableParts() where the deletable parts set to null.
But for ...
Katja Luther

03/11/2019

02:33 PM bug #8174: First test fails if term data is in loaded DataSet
This is the order how events are handled in unitils:
* [Unitils] beforeTestClass - TestClass1
* [Test] testBefore...
Andreas Müller
02:30 PM bug #8174 (New): First test fails if term data is in loaded DataSet
This is because the unitils/dbunit JpaModul starts the application context only during
~~~ java
beforeTestMethod...
Andreas Müller
01:53 PM bug #8170: javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource does not c...
I Opened the issue #8171 only for fixing the most severe problem quickly by storing the new connection in the cache f... Andreas Kohlbecker
01:41 PM bug #8170 (Feedback): javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource...
Is this still an open issue after #8171 is solved now.
I also do not fully understand the solution. In #8171 you s...
Andreas Müller
01:41 PM bug #8149: ReferenceEditor: filter inReferences ONLY by applicable reference type suppess Generic...
Related problem:
if e.g. "Phytotaxa" is tiped into the dopdown menue field, "Phytotaxa" is not selected, I have to s...
Wolf-Henning Kusber
01:10 PM feature request #6413 (In Progress): [DISCUSS] How to create type duplicates (e.g. isotypes) for ...
Patrick Plitzner
12:59 PM feature request #8173 (In Progress): spring profile remoting enabled by default
Andreas Kohlbecker
12:55 PM feature request #8173 (Resolved): spring profile remoting enabled by default
Applied in changeset commit:cdmlib|5ab0f6455f6cb83bfba0bb5ad6aee6e210d8dd14. Andreas Kohlbecker
12:48 PM feature request #8173 (In Progress): spring profile remoting enabled by default
Andreas Kohlbecker
12:40 PM feature request #8173 (Closed): spring profile remoting enabled by default
the spring profile still needs to be enabled by passing `-Dspring.profiles.active=remoting` to cdm-remote instances.... Andreas Kohlbecker
12:57 PM feature request #8096 (Resolved): Implement CacheUpdater as long running task with correct progre...
please review Katja Luther
12:54 PM bug #8171 (Resolved): javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSourc...
Applied in changeset commit:cdmlib|ddaf22cfc36cad56b677c8fecd8eb3e83db5cefb. Andreas Kohlbecker
12:13 PM bug #7874: TeamOrPersonBase entity can become unusable due to replacement of the title caches on ...
fixed a small bug in updateCaches of Team.java which results in the result was always true. commit:cdmlib|694f0ef28f3... Katja Luther

03/08/2019

07:17 PM feature request #8172 (New): Discuss: Cite an image of the holotype
Probem: in Micoalgae, a type specimen can be designated, but nobody knows how the taxon looks like. E.g. Two differen... Wolf-Henning Kusber
05:17 PM bug #8132: phycobank cdm-server instance problems with db connections
Another situation in which a connection is being opened but not properly closed is occurring in the `DataSourceConfig... Andreas Kohlbecker
02:02 PM bug #8132: phycobank cdm-server instance problems with db connections
debugging the cdm-server to find connections that have been opened but which are not being closed properly (DebugC3P0... Andreas Kohlbecker
05:06 PM bug #8171 (Closed): javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource ...
When the existing cached connection in the WrappedCdmDataSource is null a new connection will be created but is not s... Andreas Kohlbecker
04:59 PM bug #8170 (Feedback): javax.sql.DataSource.getConnection() implementation in WrappedCdmDataSource...
the documentation of `javax.sql.DataSource.getConnection()` reads like *"**Attempts to establish** a connection with ... Andreas Kohlbecker

03/07/2019

03:26 PM bug #8169 (New): avoid factory.openSession() in DaoBase

In DaoBase using `factory.openSession()` is plain wrong, the HibernateTransactionManger should be used instead.
Andreas Kohlbecker
03:24 PM bug #7106 (In Progress): avoid factory.openSession() in CdmRepository
Andreas Kohlbecker
02:17 PM bug #7106: avoid factory.openSession() in CdmRepository
since February 25th there are only occurrences related to this issue in the log which affected the phycobank code.
W...
Andreas Kohlbecker
07:25 AM bug #7106: avoid factory.openSession() in CdmRepository
with the logging of the stacktrace it now becomes clear where the unmanaged sessions are being created:
~~~~
java...
Andreas Kohlbecker
12:37 PM bug #8132: phycobank cdm-server instance problems with db connections
The problem just occurred again. This time no one was using the Taxeditor since the instance has been started.
The...
Andreas Kohlbecker
11:21 AM task #8168 (New): Check if withdrawing of per entity permission is working correctly for inRefere...
Andreas Kohlbecker
11:17 AM bug #8167 (New): Permission denied for Submitter when adding section to newly created journal

~~~
[phycobank] 2019-03-07 09:56:41,648 ERROR [qtp1510067370-69] [org.hibernate.internal.SessionImpl] - HHH000346:...
Andreas Kohlbecker
09:39 AM task #8118: Update MySQL drivers
Andreas Müller wrote:
> Some solution is setting on command line e.g. for Central European time (CET):
>
> mysql>...
Katja Luther

03/06/2019

08:57 PM task #8118: Update MySQL drivers
Some solution is setting on command line e.g. for Central European time (CET):
mysql> SET GLOBAL time_zone = '+1:0...
Andreas Müller
08:19 PM task #8118: Update MySQL drivers
Katja, I think you also had the problem localy. What did you do to fix it? Andreas Müller
08:11 PM task #8118: Update MySQL drivers
This is what I currently get when connecting to MySQL on PESIHPC:
~~~
Caused by: com.mysql.cj.exceptions.InvalidC...
Andreas Müller
08:06 PM task #8118: Update MySQL drivers
https://stackoverflow.com/questions/26515700/mysql-jdbc-driver-5-1-33-time-zone-issue Andreas Müller
05:00 PM bug #7106: avoid factory.openSession() in CdmRepository
In a locally running cdmserver started vi the eclipse launcher *cdm-server - start from war* multiple occurrences can... Andreas Kohlbecker
01:56 PM task #8166 (Closed): Adapt dataportal to term structure changes
the dataportal needs to be adapted to the changes applied in the context of #6794 Andreas Kohlbecker
01:05 PM task #8162: Move term related classes from model.common to model.term
Andreas Müller wrote:
> Other classes to move: Sources und IntextReferences, Rights, IReferencedEntity, ReferencedE...
Andreas Müller
01:03 PM task #8162: Move term related classes from model.common to model.term
Also move FeatureNode and FeatureTree to new term package as they become TermTreeNode and TermTree Andreas Müller
10:49 AM task #8130: Check if related feature data is cleared when supported facts type is changed
Katja, could you please check how we do these "model validations" in terms of e.g. nomenclatural code changes in Taxo... Andreas Müller
10:14 AM task #8130 (Feedback): Check if related feature data is cleared when supported facts type is changed
Andreas Müller wrote:
> We may want to implement hard or soft validation for this. Maybe also an update script to re...
Patrick Plitzner
10:07 AM task #8130 (In Progress): Check if related feature data is cleared when supported facts type is c...
Patrick Plitzner
10:44 AM feature request #8165 (New): enable log4j jmx for cdm-server
having the log4j jmx beans enabled would be a great help during debugging of the production server and other systems
...
Andreas Kohlbecker
10:23 AM bug #5632: ClassNotFoundException for org.eclipse.jetty.servlet.listener.ELContextCleaner during ...
Moving the ticket back to decide what we want to do with it Patrick Plitzner
10:19 AM bug #5632: ClassNotFoundException for org.eclipse.jetty.servlet.listener.ELContextCleaner during ...
This exception is still thrown when the test is run.
This is the log of the last jenkins run: http://int.e-taxonom...
Patrick Plitzner
08:51 AM bug #8164 (New): ClassNotFoundException during deserialization for Reference
Andreas K.: "Ich habe in dem Produktions-Server-Log seit Oktober 10x
`org.springframework.web.util.NestedServletEx...
Patrick Plitzner

03/05/2019

05:39 PM task #8162: Move term related classes from model.common to model.term
Andreas Müller wrote:
> we should also adapt persistence layer
done
Andreas Müller
12:43 PM task #8162 (Resolved): Move term related classes from model.common to model.term
Applied in changeset commit:taxeditor|974d02d015234ec80816dfb47eaabde6688c2fa9. Andreas Müller
12:24 PM task #8162 (In Progress): Move term related classes from model.common to model.term
Andreas Müller
12:23 PM task #8162: Move term related classes from model.common to model.term
we should also adapt persistence layer Andreas Müller
12:12 PM task #8162 (Resolved): Move term related classes from model.common to model.term
Applied in changeset commit:taxeditor|b9dc6bb1d38897b06888836dd74d48684f73c5d5. Andreas Müller
10:52 AM task #8162: Move term related classes from model.common to model.term
Other classes to move: Sources und IntextReferences, Rights, IReferencedEntity, ReferencedEntityBase, Language? Andreas Müller
05:22 PM bug #8132: phycobank cdm-server instance problems with db connections
Results from the server log:
The problem occurred again. The jdbc connection which was being used by the tread `qt...
Andreas Kohlbecker
02:58 PM bug #8107 (Closed): NPE when throwing PopupEditorException in AbstractPopupEditor
issue is not reproducible - closing. Andreas Kohlbecker
11:49 AM feature request #8163 (Rejected): RegistrationService.setStatus() method implemented
This method need to be used by the RegistrationWorkingsetPresenter.saveRegistrationStatusChange() method in cdm-vaadi... Andreas Kohlbecker
11:21 AM bug #8161 (Rejected): *FilterablePagingProvider classes as transactional readonly spring beans
the *FilterablePagingProviders only are using service methods which are anyway annotated with `@Transactional(readOnl... Andreas Kohlbecker
11:21 AM bug #7945 (Rejected): TaxonNamePopupEditor: missing genus causes exception when updating name par...
the *FilterablePagingProviders only are using service methods which are anyway annotated with `@Transactional(readOnl... Andreas Kohlbecker
11:14 AM bug #8075 (In Progress): multiple cascade all-delete-orphan exceptions related to DefinedTermBase...
Andreas Kohlbecker
10:55 AM bug #8158: cascade="all-delete-orphan" problem when ....
potentially duplicate of #8160 Andreas Kohlbecker

03/04/2019

03:19 PM task #8162 (Closed): Move term related classes from model.common to model.term
This means moving the following model classes:
* DefinedTerm
* DefinedTermBase
* OrderedTerm
* OrderedTermBase
...
Andreas Müller
03:06 PM bug #7881: reference selection combobox broken after error in ...
potentially duplicate of #8161 Andreas Kohlbecker
03:04 PM bug #7945: TaxonNamePopupEditor: missing genus causes exception when updating name parts visibility
potentially duplicate of #8161 Andreas Kohlbecker
03:00 PM bug #8065: HibernateException: corrupt session problem breaks SpecimenTypeDesignationworkingsetEd...
potentially duplicate of #8160 Andreas Kohlbecker
02:07 PM bug #8160 (Resolved): CdmBeanItemContainerFactory as readonly service bean
Andreas Kohlbecker
12:43 PM bug #8160 (Closed): CdmBeanItemContainerFactory as readonly service bean
Turning the CdmBeanItemContainerFactory into a readonly service bean should solve the cascade="all-delete-orphan" pro... Andreas Kohlbecker
12:47 PM bug #8161 (Rejected): *FilterablePagingProvider classes as transactional readonly spring beans
Turing the TaxonNameStringFilterablePagingProvider into a readonly service bean should solve the cascade="all-delete-... Andreas Kohlbecker
11:52 AM task #4600 (New): Investigate and implement tests for security in cdm-vaadin
Andreas Kohlbecker
11:51 AM task #4600 (In Progress): Investigate and implement tests for security in cdm-vaadin
Andreas Kohlbecker
11:47 AM bug #7879: Book CacheStrategy does not show 'place published', 'publisher', 'editor'
Hi Andreas, I am passing this to you since it is a bug in the cache strategy and closely related to #1866 Andreas Kohlbecker
11:39 AM feature request #8124 (Resolved): Activate Name Facts in Taxeditor
please review Katja Luther
07:42 AM task #8159 (New): Replace LocalSelectionTransfer for DnD operations
Using LocalSelectionTransfer is in most cases too generic. It is better to define an own TransferData and assign the ... Patrick Plitzner

03/01/2019

11:05 PM feature request #6794: Improve term structure
Current idea for a solution:
Collections:
* Common base class TermCollection(Base) for all Vocabularies and Gra...
Andreas Müller
04:05 PM bug #8132: phycobank cdm-server instance problems with db connections
It seems as if this problem is being cased by the CdmFilterablePagingProvider which might open an new Sesscion which ... Andreas Kohlbecker
02:46 PM bug #8132: phycobank cdm-server instance problems with db connections
this here https://stackoverflow.com/questions/34408362/c3p0-connection-pool-gives-connection-timeout-error-with-this-... Andreas Kohlbecker
01:58 PM bug #8132: phycobank cdm-server instance problems with db connections
Andreas Kohlbecker wrote:
> I set `testConnectionsOnCheckIn=true` temporarily via jmx in order to test if this helps...
Andreas Kohlbecker
11:13 AM task #615 (Closed): remove suns repository
the repository
~~~xml
<!-- sun repository -->
<repository>
<id>java.net</id>
<url>http:...
Andreas Kohlbecker
11:11 AM task #615 (Resolved): remove suns repository
Applied in changeset commit:cdmlib|d402220f823edfb01ec9385d20117d6afee9a77d. Andreas Kohlbecker
10:17 AM feature request #8150 (Resolved): Allow editing the representation label of characters in details...
Patrick Plitzner
07:17 AM bug #8158 (Closed): cascade="all-delete-orphan" problem when ....
I seem to remember that I did the following:
1. RegistrationWorkingsetEditor at http://api.phycobank.org/phycobank...
Andreas Kohlbecker

02/28/2019

09:54 PM feature request #8157 (New): Registration list view: sort registrations by the same order as in t...
newer registrations should come first.
Oder by created when! (agreed)
Andreas Kohlbecker
09:50 PM feature request #8156: Registration items show type status in bold letters
should be easy to implement, thus i am setting the priority to high Andreas Kohlbecker
09:50 PM feature request #8156 (New): Registration items show type status in bold letters
The type status in registration items is not easy to see. Making the status bold would improve the readability. Andreas Kohlbecker
09:47 PM feature request #8155 (Feedback): SpecimenTypeDesignationEditor: allow choosing the typified name...
Andreas Kohlbecker
09:47 PM feature request #8155: SpecimenTypeDesignationEditor: allow choosing the typified name from the h...
For how urgent do you consider this feature, Henning? I guess this situation will occur quite frequently? Andreas Kohlbecker
09:42 PM feature request #8155 (Feedback): SpecimenTypeDesignationEditor: allow choosing the typified name...
In case of lecto-, epit- and neo-types the SpecimenTypeDesignationEditor should selecting the typified name from the ... Andreas Kohlbecker
05:30 PM bug #7514: Change direct and inverse symbol for pro parte synonym and misapplied name relationshi...
the test page http://int.e-taxonomy.eu/dataportal/integration/reference/cdm_dataportal/taxon/c6716cee-2039-4ba8-a239-... Andreas Kohlbecker
04:12 PM bug #8154 (Worksforme): NameController.doGetTaggedName fails due to [UPDATE] not permitted for '...
http://160.45.63.173:8081/phycobank/name/a2b01d35-fdcf-43fb-8376-f03f195c6e06/taggedName.json
fails every ~4 times...
Andreas Kohlbecker
03:05 PM bug #8152 (Duplicate): ReferencePopupEditor: inReference field allows to select references with t...
Henning: References with type 'Generic' must not be in the list, filter only by matching type
So this is a duplica...
Andreas Kohlbecker
01:05 PM bug #8152 (Duplicate): ReferencePopupEditor: inReference field allows to select references with t...
Heba reported an error which was due the Journal "Rickia" having the Referencetype 'Generic'
The reference could b...
Andreas Kohlbecker
01:30 PM feature request #8153 (Closed): Adapt cdmlib to FeatureNode/FeatureTree model changes
* Since the introduction of term trees with the last model change (5.6.0) `FeatureNode.getFeature()` is deprecated an... Patrick Plitzner
12:16 PM feature request #4611 (New): I18n for the Taxeditor
sorry, was a mistake Andreas Müller
12:12 PM feature request #4611 (Resolved): I18n for the Taxeditor
Andreas Müller
12:14 PM feature request #8124: Activate Name Facts in Taxeditor
Katja Luther wrote:
> when activating the name facts for the name displayed in the details view, the details view is...
Katja Luther
11:24 AM feature request #8124: Activate Name Facts in Taxeditor
when activating the name facts for the name displayed in the details view, the details view is the selectionProviding... Katja Luther
11:57 AM bug #7107: "Omit level" in distribution hierarchy should not supress distributions source referen...
OK Andreas Kohlbecker
11:52 AM bug #7107 (New): "Omit level" in distribution hierarchy should not supress distributions source r...
Ich glaube nicht, dass das für E+M relevant ist, da wir in E+M ja das E+M Voc verwenden, welches keine Omit levels ha... Andreas Müller
11:37 AM bug #7107 (Feedback): "Omit level" in distribution hierarchy should not supress distributions sou...
Hallo Andreas, ich denke das ist auch für Euro+Med releveant, oder?
Wenn ja, sollten wir das Tag hinzufügen und di...
Andreas Kohlbecker
11:57 AM feature request #4610: [DISCUSS] I18n for the EDIT platform
Please do not move unreviewed tickets to Reviewed milestone Andreas Müller
11:05 AM bug #8151 (Resolved): after creating a new synonym and pasting a name string the default string i...
the call of placeCursor() caused that the cursor was at the end of the "Klicken, um ..." string. Removing this method... Katja Luther
10:58 AM bug #8151 (Closed): after creating a new synonym and pasting a name string the default string is ...
mail von S. v. M.:
Beim Reinkopieren eines neuen Synonyms blieb der Text “Klicken, um Namen hinzuzufügen” stehen.
...
Katja Luther
08:07 AM feature request #8146: Adapt taxeditor UI to structure and property term type
Add character to term menu with commit:2c98dda6165033a58c7df8c06b21518d380307b3 Patrick Plitzner

02/27/2019

03:52 PM bug #8132: phycobank cdm-server instance problems with db connections
I set `testConnectionsOnCheckIn=true` temporarily via jmx in order to test if this helps avoiding this connectivity p... Andreas Kohlbecker
03:30 PM feature request #8124: Activate Name Facts in Taxeditor
for the name bulk editor the name facts are activated now.
still missing is the activation if name is selected in ...
Katja Luther
02:24 PM feature request #8150 (Closed): Allow editing the representation label of characters in details view
Patrick Plitzner
01:56 PM feature request #8136 (In Progress): Implement sources for type designations in TaxEditor
Katja Luther
10:34 AM bug #8149 (Closed): ReferenceEditor: filter inReferences ONLY by applicable reference type suppes...
In reference type = article
Drop down of Journals should only search for entries = journal (not for all references)
...
Wolf-Henning Kusber
10:19 AM bug #8148 (In Progress): Login Dialog cuts off information
Katja Luther
10:18 AM bug #8148 (Resolved): Login Dialog cuts off information
Applied in changeset commit:taxeditor|a08af9f9d2b8840b48fc63b647aca9ee0a34b68c. Katja Luther
09:38 AM bug #8148 (Closed): Login Dialog cuts off information
In the case of an exception and for the advanced section information is not correctly displayed.
![](picture896-1....
Patrick Plitzner
09:34 AM feature request #8147 (Resolved): Add "plural" to representation detail element
Fixed with commit:taxeditor|754fbf873ca0b63addc6842c089298fff76eb30d Patrick Plitzner
08:44 AM feature request #8147 (Closed): Add "plural" to representation detail element
Patrick Plitzner
08:37 AM feature request #8146 (Closed): Adapt taxeditor UI to structure and property term type
1. ~~Add term editor menu for each~~
1. ~~Restrict tree selection in CharacterEditor~~
1. ~~Restrict context menu,...
Patrick Plitzner
 

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